SKATv: Sequence kernel association test (SKAT) using variant test...
In baolinwu/mkatr: Miscellaneous variant-set association test methods

Description Usage Arguments Details Value References

Reproduce the SKAT p-value (from the SKAT R package) using marginal variant score statistics

1	SKATv(obj, G, W.beta = c(1, 25))

`obj`	a fitted null model using KAT.null() or KAT.cnull()
`G`	genotype matrix, sample in rows, variant in columns
`W.beta`	Beta parameters for variant weights

We compute the SKAT based on the variant test statistics (typically of much smaller dimension), which leads to much more efficient computations. The same algorithm as the SKAT R package is used to compute the tail probability of 1-DF chi-square mixtures.

SKAT p-value

Wu, M.C., Lee, S., Cai, T., Li, Y., Boehnke, M., and Lin, X. (2011) Rare Variant Association Testing for Sequencing Data Using the Sequence Kernel Association Test (SKAT). American Journal of Human Genetics, 89, 82-93.

Wu,B., Guan,W., and Pankow,J.S. (2016) On efficient and accurate calculation of significance p-values for sequence kernel association test of variant set. Annals of Human Genetics, 80(2), 123-135.

baolinwu/mkatr documentation built on May 14, 2019, 6:03 a.m.